Exploring microbial diversity in South Korean caves through shotgun sequencing: contrasting dry and wet environments, swabbing versus sediment sampling

Abstract

Caves host bacterial communities that represent diverse and unique ecosystems, often isolated from external influences. Diversity among bacterial colonies can vary greatly depending on the cave’s geographical location but it is also linked to the environmental conditions inside the cave such as a depth gradient, light and humidity levels, nutrients availability and substrate conditions. Microbes in caves have adapted to live under extreme conditions and because of that have often developed unique metabolic pathways. In this present work, metagenomics sequence data from five South Korean caves are analyzed with the main objective of identifying microbial taxa as potential proxies for cave environmental conditions. Two independent shotgun sequencing platforms have been used targeting short and long reads through Illumina and Oxford Nanopore technologies respectively. The DNA samples come from swabs of rock surfaces or sediments inside these Korean caves that can be classified as wet, dry or seasonally wet. The internal depth gradient as well as different substrates (swabs and sediments) have also been considered for the interpretation of the composition of the internal microbiota. Dry environments like those from Baram and Simbok Caves have a high abundance of species belonging to the phylum Actinobacteria, compared to wetter caves like Ondal, Sanjidang and Seodae where Proteobacteria are instead more abundant. In dark and undisturbed sectors of the caves, the microbial colonies are dominated by Gammaproteobacteria compared to areas near the entrance. © © The Geological Society of Korea 2024.